Structure of PDB 5mc4 Chain B

Receptor sequence

>5mc4B (length=473) Species: 9606 (Homo sapiens)

GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVC
REASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEAHRE
VMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICAVLHYGHAGAPND
RTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAVYEAVLRSSR
AVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLGAVFM
PHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPG
IYFIDHLLDEALADPARASFLNREVLQRFRGFGRVRIEEDVVVTDSGIEL
LTCVPRTVEEIEACMAGCDKAFT

3D structure

• PDB: 5mc4 Structural basis for prolidase deficiency disease mechanisms.
• Chain: B
• Resolution: 1.8 Å

Enzymatic activity

• Enzyme Commision number: 3.4.13.9: Xaa-Pro dipeptidase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MN	B	D287 H370 E412 E452	D273 H356 E398 E438
BS02	MN	B	Y241 D276 D287 E452	Y233 D262 D273 E438
BS03	GLY	B	Y241 D287 H377	Y233 D273 H363
BS04	PRO	B	H366 H377 R398	H352 H363 R384

Gene Ontology

Molecular Function

• GO:0004181 metallocarboxypeptidase activity
• GO:0005515 protein binding
• GO:0008233 peptidase activity
• GO:0008237 metallopeptidase activity
• GO:0016805 dipeptidase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding
• GO:0070006 metalloaminopeptidase activity
• GO:0102009 proline dipeptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0006520 amino acid metabolic process
• GO:0030574 collagen catabolic process
• GO:0043069 negative regulation of programmed cell death

Cellular Component

• GO:0070062 extracellular exosome

External links

• PDB: RCSB:5mc4, PDBe:5mc4, PDBj:5mc4
• PDBsum: 5mc4
• PubMed: 30066404
• UniProt: P12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)